Whole Foods said Tuesday that it has purchased 84.1% of Wild Oats’ stock through its $18.50-a-share tender offer, and it plans to buy another 12.7% in the next three days. The remainder of the stock will be purchased via a short-form merger.

The $565 million deal, announced in February, was originally slated to close in April. The Federal Trade Commission, however, attempted to block the transaction on the belief that it would form an organic-foods monopoly.

Whole Foods and Wild Oats contended that traditional chains like Safeway (SWY — Cramer’s Take — Stockpickr) and Kroger (KR — Cramer’s Take — Stockpickr) already have a significant presence in the natural-foods space. A district court judge ruled in favor of the companies, and the FTC last week lost its request for an emergency stay of the deal.

“While closing this merger has taken longer than we anticipated, we are very excited to now begin the integration process,” said Whole Foods Chairman and CEO John Mackey.

“We have found it generally takes up to two years to transition to our decentralized operations and implement our incentive programs,” he said. “We expect this acquisition to be similar and that over time we will recognize significant synergies through G&A cost reductions, greater purchasing power, increased utilization of our facilities and new team member talent.”

Shares of Whole Foods recently were down 53 cents, or 1.2%, to $45.22.

We will see soon what happens in terms of store closures and system changes. One of the key questions is how will they treat the Wild Oats employees? The store level folks will probably be fine if they don’t close their stores as Whole Foods will need them.

The future of the Wild Oats headquarters staff is less certain. Since Whole Foods is growing, it needs good people and may find opportunities to use them. Whole Foods certainly has an incentive to do so because with mainstream grocers all going organic and health-oriented, Whole Foods would rather not release the talent that has real experience to the mainstream retailers.

Catch of the day is definitely Pundit contributor (see here and here) and Wild Oats Vice President for Produce and Floral, Don Harris.

After a career at Safeway, Don, almost uniquely for high end executives of major chains, made the transition to an organic/natural/health-oriented concept. With a finger on the pulse of the organic consumer and a head able to organize mass procurement, distribution and sales, a man and a moment have met. He could build the program at any mainstream retailer. We will see how Whole Foods handles the situation.

In fact, a lot of people will be watching. Although one of its “core values” as “supporting Team Member happiness and excellence” and its web site trumpets that Whole Foods is “…creating a respectful workplace where people are treated fairly and are highly motivated to succeed,” everyone will be looking to see if Whole Foods’ CEO John Mackey will be living up to the company’s stated mission.

After all, when word came out of the news that Mackey was posting anonymously on web boards knocking Wild Oats, the nagging concern was that, in the end, he was just another suit. He wasn’t posting on organic boards about the product; he was posting on stock boards.

This type of perception could alienate a Whole Foods customer. So how Whole Foods is seen to be treating the people from the Wild Oats acquisition will play a big role in establishing how consumers perceive this new, larger, Whole Foods.